igraph对象可以具有有向边和无向边吗? [英] Can an igraph object have directed and undirected edges?

问题描述

我正在尝试使用igraph/ggraph绘制网络，其中某些边是定向的，而其他边则不是.

I am trying to use igraph/ggraph to plot a network, in which some of the edges are directed and others are not.

我的边缘列表中的一个小例子.在这里，我想将蛋白质位点的边缘表示为无向的，而将磷酸化的边缘表示为有向的.

A small example from my edgelist. Here the protein-site edges are what I want to represent as undirected and the phosphorylation edge as directed.

df <- data.frame(
  stringsAsFactors = FALSE,
              from = c("RPS6KA3", "RPS6KA3", "RPS6KA3", "RPS6KA3", "RPS6KA3"),
                to = c("RPS6KA3_Y529-p",
                       "RPS6KA3_S227-p","RPS6KA3_S369-p","RPS6KA3_T577-p","ATF4"),
            action = c("protein-site","protein-site",
                       "protein-site","protein-site","phosphorylation")
)

我尝试将无方向的边缘设置为子集，并指定它们的原样，但这没有用:

I have tried subsetting the undirected edges and specifying them as such, but it didn't work:

library(igraph)
nw <- graph_from_data_frame(df)

E(nw)[E(nw)$action == "protein-site"] <- as.undirected(subgraph.edges(nw, E(nw)[E(nw)$action == "protein-site"] ))

还有其他建议吗? 正如我所说的，我真的只想绘制此图(使用ggraph).

Does anyone have any other suggestions? As I say, I am really only wanting to plot this (using ggraph).

谢谢！

推荐答案

如果愿意使用igraph进行绘制，则可以按照指示导入边缘列表，然后使用edge.arrow.mode.

If you would be willing to plot with igraph you can import the list of edges as directed and then use edge.arrow.mode.

nw <- graph_from_data_frame(df, directed = T)


plot(nw)

plot(nw,
     edge.arrow.mode = ifelse(E(nw)$action=="protein-site", "-", ">"))

我不确定ggraph是否支持任何类似内容.我认为可能可以更改箭头的大小，并为无方向的边缘将其设置为0.这是行不通的，因为箭头继承了边缘其余部分的样式.

I am not sure ggraph supports anything similar. I thought it might be possible to change the size of the arrows, and set it to 0 for undirected edges. This doesnt work, as arrows inherit the style of the rest of the edge.

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